PubMed Mapping Tester
Why PubMed Mapping Tester?
With Automatic Term Mapping, a simple text query is translated to a more complex one, often composed of MeSH headings as well as different text fields. The algorithm for doing so is maintained by the National Library of Medicine, and the final translation for a given search is viewable by selecting the "Advanced" tab in PubMed. To take one completely random example, the mapping for the term "covid-19" becomes this:
"covid 19"[All Fields] OR "covid 19"[MeSH Terms] OR "covid 19 vaccines"[All Fields] OR "covid 19 vaccines"[MeSH Terms] OR "covid 19 serotherapy"[All Fields] OR "covid 19 serotherapy"[Supplementary Concept] OR "covid 19 nucleic acid testing"[All Fields] OR "covid 19 nucleic acid testing"[MeSH Terms] OR "covid 19 serological testing"[All Fields] OR "covid 19 serological testing"[MeSH Terms] OR "covid 19 testing"[All Fields] OR "covid 19 testing"[MeSH Terms] OR "sars cov 2"[All Fields] OR "sars cov 2"[MeSH Terms] OR "severe acute respiratory syndrome coronavirus 2"[All Fields] OR "ncov"[All Fields] OR "2019 ncov"[All Fields] OR (("coronavirus"[MeSH Terms] OR "coronavirus"[All Fields] OR "cov"[All Fields]) AND 2019/11/01:3000/12/31[Date - Publication])
The other way to see the results of a search (and the mapping from which it is derived) is by using the API maintained by the NCBI. While the new version of PubMed has been in production for some months, the public API still points to the old search interface (and thus, the older iteration of ATM).
How does it work?
Happily, there is now a test instance of the API that points to the new search interface, allowing us to directly compare one version to the other (for at least the next several weeks before the old API is retired). It is these two different APIs that PubMed Mapping Tester uses to retrieve the two sets of results for comparison.
Once you enter your search, you'll see the number of results returned by both 'old' PubMed and the current version. You'll also see the ATM translation used by each. Any terms that are newly included in the new mapping will be highlighted in yellow. For example, here is the mapping for 'influenza' compared in each system:
Count: 121778
Mapping:
"influenza, human"[MeSH Terms] OR ("influenza"[All Fields] AND "human"[All Fields]) OR "human influenza"[All Fields] OR "influenza"[All Fields]
Count: 148033 (21.56% more)
Mapping:
"influenza s"[All Fields] OR "influenza, human"[MeSH Terms] OR ("influenza"[All Fields] AND "human"[All Fields]) OR "human influenza"[All Fields] OR "influenza"[All Fields] OR "influenzas"[All Fields] OR "influenzae"[All Fields]
Technology and Credits
This application is made with JavaScript and runs in your browser.
PubMed is queried (and results are retrieved) using the National Center for Biotechnology Information's publicly accessible E-utilities API.
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